Luciano Andres Abriata

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Related publications (71)

Assessing the potential of atomistic molecular dynamics simulations to probe reversible protein-protein recognition and binding

Matteo Dal Peraro, Luciano Andres Abriata

Protein-protein recognition and binding are governed by diffusion, noncovalent forces and conformational flexibility, entangled in a way that only molecular dynamics simulations can dissect at high resolution. Here we exploited ubiquitin's noncovalent dime ...

Nature Publishing Group2015

A coiled coil switch mediates cold sensing by the thermosensory protein DesK

Thomas Lemmin, Matteo Dal Peraro, Luciano Andres Abriata

The thermosensor histidine kinase DesK from Bacillus subtilis senses changes in membrane fluidity initiating an adaptive response. Structural changes in DesK have been implicated in transmembrane signaling, but direct evidence is still lacking. On the basi ...

Wiley-Blackwell2015

The importance of dynamics in integrative modeling of supramolecular assemblies

Matteo Dal Peraro, Luciano Andres Abriata, Giorgio Elikem Tamo

Revealing the atomistic architecture of supramolecular complexes is a fundamental step toward a deeper understanding of cellular functioning. To date, this formidable task is facilitated by an emerging array of integrative modeling approaches that combine ...

Current Biology Ltd2015

Molecular dynamics simulations of apocupredoxins: insights into the formation and stabilization of copper sites under entatic control

Matteo Dal Peraro, Luciano Andres Abriata

Cupredoxins perform copper-mediated long-range electron transfer (ET) in biological systems. Their copper-binding sites have evolved to force copper ions into ET-competent systems with decreased reorganization energy, increased reduction potential, and a d ...

Springer2014

Dissecting the Effects of Concentrated Carbohydrate Solutions on Protein Diffusion, Hydration, and Internal Dynamics

Francesco Piazza, Matteo Dal Peraro, Enrico Spiga, Luciano Andres Abriata

We present herein a thorough description of the effects of high glucose concentrations on the diffusion, hydration and internal dynamics of ubiquitin, as predicted from extensive molecular dynamics simulations on several systems described at fully atomisti ...

Amer Chemical Soc2014

A dimerization interface mediated by functionally critical residues creates interfacial disulfide bonds and copper sites in CueP

Matteo Dal Peraro, Luciano Andres Abriata

CueP confers bacterial copper resistance in the periplasm, particularly under anaerobic conditions, through an unknown mechanism. The only available structure and limited solution data suggest that CueP forms noncovalent timers in solution, whereas sequenc ...

Elsevier Science Inc2014

Tuning the electronic structure of the Cu-A center by second sphere coordination mutations

Luciano Andres Abriata

Springer2014

Investigation of non-corrin cobalt(II)-containing sites in protein structures of the Protein Data Bank

Luciano Andres Abriata

Protein X-ray structures with non-corrin cobalt(II)-containing sites, either natural or substituting another native ion, were downloaded from the Protein Data Bank and explored to (i) describe which amino acids are involved in their first ligand shells and ...

Wiley-Blackwell2013

All-atom simulations of crowding effects on ubiquitin dynamics

Matteo Dal Peraro, Enrico Spiga, Luciano Andres Abriata

It is well-known that crowded environments affect the stability of proteins, with strong biological and biotechnological implications; however, beyond this, crowding is also expected to affect the dynamic properties of proteins, an idea that is hard to pro ...

Iop Publishing Ltd2013

Analysis of copper-ligand bond lengths in X-ray structures of different types of copper sites in proteins

Luciano Andres Abriata

An updated picture of the ligand sets and copper-ligand atom bond lengths in proteins is presented which takes advantage of (i) the approximately twofold increase in the number of entries for copper-containing proteins in the PDB since the last study of th ...

Wiley-Blackwell2012

Utilization of NMR spectroscopy to study biological fluids and metabolic processes: Two introductory activities

Luciano Andres Abriata

This work describes two activities designed to introduce students into the use of NMR spectroscopy for the analysis of biological fluids. In the first activity, 1H spectra of common beverages are acquired and analyzed to identify their most abundant consti ...

Wiley-Blackwell2012

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